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Description

In microscopy, the field of view is limited and depends on the objective magnification. With growing applications of microscopic imaging and spatial analysis, digitally capturing large montages of a sample is often required. Automated microscope stages facilitate the production of accurate montages of a given sample. Unfortunately, the cost of entry level automated microscope stages (>$10,000) is prohibitive to many researchers. This project provides an alternative to consumer options at relatively low cost (

Details

The microscope used in this project is an Olympus Bx40 with a third-party digital camera. Stagmo, is secured to the existing microscope stage, and stepper motors are utilized to control the existing manual stage control knobs. Stagmo does not require any modification of existing microscope systems, but "straps" on and hijacks existing controls. This makes Stagmo ideal for traveling researchers or graduate students who are using other facilities equipment. A simple button interface is used to input the dimensions of the microscopic sample into an Arduino. Stagmo utilizes input dimensions to precisely move the microscope stage every few seconds, and triggers the camera controller on the computer capture an image of the current microscope field and output the image to a specified directory. The path, rows and columns utilized by Stagmo to capture the image are output with the image file into imageJ. The image stitching plug-in by Stephan Preibisch (http://fly.mpi-cbg.de/~preibisch/software.html#Stitching ) is used to assemble the images in the directory into a montage. Since the precise location of each image is specified by Stagmo, this process is minimizes the computation load required to produce large montages.

The current version of Stagmo can be greatly enhanced with greater user control (integrated microscope calibration for changing objectives on the fly), improved user interface with a simple lcd to provide the current parameters and estimated time to completion, improved digital camera integration, and an improved chassis/ hardware microscope integration.

Components

1×
arduino

1×
motorshield

2×
stepper motors

4×
buttons

1×
switch
Development Kits, Boards and Systems / Development Kits and Boards

Discussions

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I've been giving this idea some thought, and if I get the chance, I might try a polar co-ordinate approach. By this I mean, make a three servo controlled platform that sits on the existing stage and rotates, shifts and lifts the slide.

I suspect this will take less effort than motorising the existing stage (I am probably wrong in this assumption).

The work flow would be something like... place slide on (clear acrylic?) block controlled by servos, one for rotation (θ), one for horizontal linear movement (h), one for vertical movement (z).

Focus manually on specimen, trigger computer to take a sequence of images by scanning using a polar co-ordinate location algorithm. Lift or lower for change of focal plane with z axis servo...

Hi, I'm based in Kampala, Uganda and am working on automated image analysis (via a microscope and a smart phone). One issue is somehow getting the microscope to focus etc. An MSc student here built some hardware to do this http://aidevmakerere.blogspot.com/2013/03/microscope-autofocus.html . One issue is that we are trying to get the costs down. The clinics have microscopes (but rarely have trained lab-techs), which is why the device might be useful, but the reliability and cost of the autofocus/translation motorisation will probably be prohibitive... (even at $100/clinic). Currently we're thinking of the app telling someone what to do (e.g. turn focus knob clockwise, etc!). This part of the project's not been developed yet, so I'm just looking for ideas.
see the blog for more details about the project: http://aidevmakerere.blogspot.com/search/label/Ocula

Wow... the Olympus Bx40 is rather impressive microscope. You've set the bar pretty high, I doubt if my results will be quite as good, but that isn't going to stop me from trying... I presume as well as moving the stage, you have some form of automatic control of the focus, so you can stack in the z axis as well as stitch in the x and y axis.

You've beaten me to it on this project, I have a bunch of microscope stages "rescued" from a local skip... two of which have been resurrected for this exact purpose. I even have the servos and an arduino clone sitting ready to start the project. I'm just missing the magic "infinite amount of spare time" ingredient. best of luck with this... I'll be following along with interest.